This document outlines the procedures and tools used in a classical molecular dynamics lab as part of MIT's course 10.637. It covers various water models, procedures for preparing and analyzing protein structures, commands for using the Slurm queue on the Maverick machine, and command-line tips for efficient navigation and file management. The content is geared towards helping students set up their computational environment and manage simulations effectively.

1. MIT
10.637
Lecture 7
Lab 2: Classical MD
hjkulik@mit.edu
9-25-14

2. MIT
10.637
Lecture 7
Lab 2 overview
water models:
TIP3P, TIP4P, TIP4P-FB, SPC/Fw
equilibration, production, and analysis
MgCl2 solution:
Choose one water model, add ions,
equilibrate, production, and analysis
Ubiquitin WT protein:
Get PDB file, prepare, solvate protein,
equilibrate, production, analysis
Ubiquitin mutant:
Mutate WT protein, solvate, equilibrate,
production, analysis

3. MIT
10.637
Lecture 7
AMBER nuts and bolts
AMBER dat files + Online repository:
force field files, prepin files, to describe
proteins, nucleotides, water, and ions.
antechamber/RED server:
generates force field and prepin files for
non-standard ligands and residues
tleap: organize and load in force field
properties, solvate, set box dimensions,
neutralize, and generate
topology/coordinate files
sander: run minimizations and molecular
dynamics using topology, coordinates, and
input parameters.
cpptraj/ptraj: process and analyze output
of trajectories.

4. MIT
10.637
Lecture 7
Using XSEDE
For those who didn’t set up aliases last time:
1) Login to the XSEDE login portal
ssh <xsede username>@login.xsede.org
2) Login to the Maverick machine
gsissh -p 2222 maverick.tacc.xsede.org
Once on Maverick, copy files as needed over from your athena machine:
scp <Athenausername>@athena.dialup.mit.edu:~/<local file name> ./
We’ll want to add a few commands to your bashrc. These are:
export AMBERHOME=/work/02958/hkulik/maverick/shared/amber/
export
LD_LIBRARY_PATH=/work/02958/hkulik/maverick/shared/amber/lib:$LD_LIB
RARY_PATH
export PATH=/work/02958/hkulik/maverick/shared/amber/bin:$PATH
You can add them by editing your ~/.bashrc:
nano ~/.bashrc
Then:
source ~/.bashrc

5. MIT
10.637
Lecture 7
tleap
Tleap takes commands or an input file.
Example input commands:
source leaprc.ff14SB
mol = loadpdb wat.pdb
check mol
solvatebox mol TIP3PBOX 14.37
savepdb mol tip3pwaterbox.pdb
saveamberparm mol tip3pwater.prmtop tip3pwater.inpcrd
quit

6. MIT
10.637
Lecture 7
Maverick SLURM queue
• Maverick uses SLURM as a queueing system.
• We write a job script and then submit it to the queueing system to run when
resources are available.
• Example job script:
#!/bin/bash
#SBATCH –J equilibration
#SBATCH –o equil.oe
#SBATCH –N 1
#SBATCH –p gpu
#SBATCH –t 12:00:00
#SBATCH –n 1
. /usr/local/etc/login
module load cuda/6.0
module load intel
#Example run command
./exec < input > output

7. MIT
10.637
Lecture 7
Maverick SLURM queue
• We issue commands to the SLURM queue to manage our jobs.
• Submit the job script:
sbatch <jobscript>
• Submit a job that depends on another one:
sbatch –d <slurm job #> <jobscript>
• Check the status of all of your jobs
showq –u <xsede username>
• Check the status of everyone’s jobs
showq
• Check specifics of a running or queued job
scontrol show job <slurm job #>
• Cancel a job
scancel <slurm job #>

8. MIT
10.637
Lecture 7
sander
Minimization example:
unrestrained_min.in:
&cntrl ! Control namelist
imin = 1, ! Minimization is on
maxcyc = 2000, ! Number of cycles to run minimization
ncyc = 2000, ! Number of cycles to run steepest descent
ntb = 1, ! Constant volume PBCs
cut = 9.0, ! Nonbonded cutoff distance in Angstroms-this
is a little small, but our simulation cell is a bit small.
ntxo = 2, ! NetCDF file for coordinates and restart
ioutfm = 1, ! Binary NetCDF trajectory
/

9. MIT
10.637
Lecture 7
sander
Dynamics example:
constV_equil.in:
&cntrl !Control namelist
nstlim=5000, !Number of dynamics steps
dt=0.002, !Timestep in ps**
ntx=1, !Read in the coordinates without velocities.
irest=0, !We are not restarting the simulation
ntpr=500, !How frequently we print progress
ntwr=5000, !How frequently we write the restart file
ntwx=5000, !How frequently we write the mdcrd file
tempi=100.0, !Initial temperature
temp0=298.15, !Reference target temperature- to compare to
experiment
ntt=3, !Weak coupling thermostat
gamma_ln=1.0, ! Time constant in ps for heat bath coupling.
ig=-1, !Random seed for starting velocities.
ntb=1, ! Constant volume PBCs
ntc=2, ! SHAKE algorithm to constrain bonds with hydrogen**
ntf=2, ! Interactions involving H-atoms omitted**
cut = 9.0, ! Nonbonded cutoff distance in Angstroms
ntxo=2, ! NetCDF file for coordinates and restart
ioutfm=1, ! Binary NetCDF trajectory
/

10. MIT
10.637
Lecture 7
cpptraj/ptraj
cpptraj processes our trajectory files. It takes an input file, command line
options, or work at the interactive prompt.
To start, we specify a prmtop file:
$AMBERHOME/bin/cpptraj –p <myprmtop>
Example queries:
trajin <mdcrd file>
(can take multiple mdcrd files and will sequentially load them)
trajout mdcrd.pdb pdb
radial myrdf.rdf 0.05 15.0 @O density 0.0033
distance mgcl @MG :2@CL- out mg-cl.dist
go
quit

11. MIT
10.637
Lecture 7
Working with athena
• Make sure terminal is locked to launcher.
• Pick a text editor to use and get
comfortable– nano for most of you.
• Try some basic linux commands.

12. MIT
10.637
Lecture 7
Logging into athena
• Locally: here in 14-0637
• Quick stations on campus
• Athena clusters (eg bldg 56)
– At commandline: tellme combo
• Remotely: X11 programs (eg avogadro)
will be very slow over ssh but may be
possible with fast internet at MIT.
– ssh –X <athena
username>@athena.dialup.mit.edu

13. MIT
10.637
Lecture 7
Commandline tips
ls: lists all visible files in the current directory.
Try: ls -ltrh
to view files with long printing (l), last modified sorting (t),
in reverse (r), and human readable (h) file sizes.
Try: ls .*
to view all hidden files that start with ‘.’ such as .bashrc.
Try: ls */*
to view all files in first layer of subdirectories, etc.
Try: ls */ -d
to view all files that match a wildcard with a directory.

14. MIT
10.637
Lecture 7
Commandline tips
cd: change directory.
Try: cd ~/
to change directory to home
Try: cd -
to change directory to the previous one.
Try: cd ../
to move up one directory

15. MIT
10.637
Lecture 7
Commandline tips
mkdir: make a directory.
Try: mkdir -p path/to/directory
to simulatenously make new directory path, with a subdirectory
inside to, with sub-subdirectory inside called ‘directory’
pwd: gets the current working directory.
ln: make a symbolic link for a directory.
Say you have a long source directory like
/usr/local/source/file/compiler/bin/ and want to be able to see its
contents more easily.
Try: ln -s /usr/local/source/file/compiler/bin/ easydir
to make a symbolic link in your existing directory as a
subdirectory called “easydir”.

16. MIT
10.637
Lecture 7
Commandline tips
cp/mv: copy or move files from one place to another. You may want to copy or
move files around from one place to another. Here are some examples of
copying or moving the old file apples.txt to oranges.txt.
Try: cp -i apples.txt oranges.txt
“i” for interactive means that if oranges.txt already exists, it will ask you if you
want to overwrite.
Try: mv -i apples.txt oranges.txt
“i” for interactive means that if oranges.txt already exists, it will ask you if you
want to overwrite the existing oranges.txt.
Try: mv -f apples.txt oranges.txt
“f” forces the move even if an existing oranges.txt is already there.
Try: cp -p apples.txt oranges.txt
“p” means that permissions and timestamps will be preserved.
Try: cp -r apples/ oranges/
“r” means that you’re recursively copying all the files in a directory. You need to
do this if you’re trying to copy a directory.

17. MIT
10.637
Lecture 7
Commandline tips
rm: remove a file.
Much like cp and mv, you can remove files (be
careful with this) using a couple different flags.
Try: rm -i apples.txt
to interactively ”i” remove a file (i.e. get a y/n
statement)
Try: rm -v apples.txt
to get a verbose listing of the files removed.
Try: rm -r apples/
to recursively remove an entire directory.

18. MIT
10.637
Lecture 7
Logging into XSEDE machines
• Best way:
– ssh <xsede portal username>@login.xsede.org
– enter your portal username password
– also, you can add an alias:
• In athena, probably using cshell:
– nano ~/.cshrc.mine
– alias xsede 'ssh <username>@login.xsede.org'
• In bash:
– nano ~/.bashrc
– (on a mac) nano ~/.profile
– alias xsede=‘ssh <username>@login.xsede.org’
– Once at the portal, commands for passwordless login to other machines show up in
MOTD:
• Trestles: gsissh trestles.sdsc.xsede.org
• Maverick: gsissh -p 2222 maverick.tacc.xsede.org
• Alternatives:
– You may be able to login to these machines directly (YMMV)
• ssh <portalusername>@maverick.tacc.xsede.org (likely works)
• ssh <portalusername>@trestles.sdsc.xsede.org (probably doesn’t work)

19. MIT
10.637
Lecture 7
Aliases
• Useful way to associate long linux commands
with shortcuts
• Forgot which aliases you have set? Type
alias at the commandline
• If you set aliases, you will need to reinitialize
the shell before they’re active. E.g. in bash
type ‘bash’ in cshell type ‘tcsh’ or log out and
log in again.

20. MIT
10.637
Lecture 7
Copying data
To access data from other machines, use secure copy. You may want to do this
to an open machine such as an athena machine:
Syntax from remote machine to current location:
scp <remote username>@<remote machine>:<remote file loc> <local loc>
Syntax from local machine to remote machine:
scp <local loc> <remote username>@<remote machine>:<remote dir>
You can do this by copying from Maverick/Trestles->Xsede Login->Home
machine
Or you can copy from Maverick/Trestles->Athena.

21. MIT
10.637
Lecture 7
Summary
• Review on your own, more commandline tips:
– http://hjklol.mit.edu/content/bios-203-useful-
commandline-tools
– Or check for cheat sheet on Stellar.
• Make sure you have set up your xsede
account before you leave today!
• Let’s get started next time with molecular
mechanics!
• Any questions?

22. MIT
10.637
Lecture 7
OS X
Applications>Utilities>Terminal and add to dock

23. MIT
10.637
Lecture 7
OS X